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Mangrove ecosystems are highly productive tropical coastal ecosystems which have a potentially high impact on the carbon budget of the tropical and global coastal zone. The carbon dynamics in mangrove ecosystems has been the subject of numerous studies during the past decades, but we are still far from having an integrated view of the overall ecosystem functioning in terms of organic matter processing. The application of recent analytical techniques has produced a wealth of new information but has also indicated the gaps in our knowledge on organic matter cycling in these ecosystems. This paper provides an overview of our current understanding of organic matter dynamics in mangrove ecosystems, and reviews data based on stable isotope analyses, on (i) the delineation of carbon sources in different organic matter pools, (ii) utilization patterns of organic carbon by microbial and faunal communities, and (iii) organic matter exchange between mangroves and adjacent ecosystems. Although the use of stable isotopes has a number of limitations and has not always been able to unambiguously assess source contributions, it has been invaluable in refuting some long-standing paradwigms, and has shown that source characterization is crucial in order to better estimate organic matter budgets in these dynamic ecosystems. Future studies on process rates or flux measurements should therefore ideally be combined with a variety of chemical tracers to determine the source of the organic matter considered.